Although the failure to degrade cellular RNAs contributes to neurologic disorders and to autoimmune diseases such as systemic lupus erythematosus (SLE), little is known of the molecules and pathways that degrade most aberrant RNAs in mammalian cells. Most RNA does not code for proteins, and truncated and misfolded rRNAs, tRNAs and other noncoding RNAs can be generated by gene mutations, transcriptional errors, and processing mistakes. RNAs can also be damaged by sunlight exposure and other environmental insults. Also, since 30-50% of mammalian genomes consists of repetitive elements, including active retrotransposons and their many truncated and divergent relatives that remain transcriptionally active, transcripts from these elements must be recognized and degraded. Most studies of RNA decay have been carried out in yeast, where an exonuclease complex known as the exosome is a major contributor to noncoding RNA decay. Additional pathways likely contribute in metazoans, as the accumulation of numerous aberrant noncoding RNAs that occurs when exosome subunits are mutated in yeast has not been observed when the subunits are depleted from animal cells. The objective of this project is to characterize a novel pathway by which aberrant noncoding RNAs are handled in mammalian cells and some bacteria. The focus is on the Ro 60 kD autoantigen, an important target of the immune response in patients suffering from SLE and Sjogren's syndrome and a likely participant in several clinical sequelae. Mice lacking Ro develop an autoimmune disease that resembles SLE in patients, and Ro is important for survival after UV irradiation in mammalian cells and at least one eubacterium. Ro is ring-shaped and binds newly synthesized misfolded RNAs such that their single-stranded 3'ends protrude from the Ro central cavity. In the cytoplasm, Ro binds noncoding RNAs called Y RNAs that regulate the subcellular distribution of Ro. In at least one bacterium, Ro and a Y RNA form a complex with a ring-shaped exonuclease, polynucleotide phosphorylase (PNPase), that functions in rRNA degradation during nutritional stress. Our first aim is to test the hypothesis, based on electron microscopy of the bacterial complex, that single-stranded RNA threads through the Ro ring into the PNPase cavity and that the Y RNA scaffolds the complex. Our second aim is to determine the extent to which Ro modulates expression of aberrant transcripts in mouse cells. We will test the hypothesis, based on cross-linking of Ro to bound RNAs in mouse embryonic stem cells, that Ro functions in the decay of transcripts from repetitive elements. Our third aim is to identify the direct targets of Ro following exposure of mammalian cells and bacteria to UV irradiation. Together, these studies should elucidate a novel mechanism for modulating RNA decay by exonucleases, illuminate the role of a clinically important RNA-binding protein in mammalian RNA metabolism, and could yield insights into the roles of noncoding RNA metabolic pathways in adapting RNA populations during stress, a poorly understood but likely important part of maintaining cellular homeostasis. PUBLIC HEALTH RELEVANCE: Antibodies against an RNA-binding protein called the Ro 60 kDa autoantigen are associated with sunlight- sensitive skin lesions in adults with systemic lupus erythematosus and with similar skin rashes and permanent heart defects in babies of mothers with these antibodies. After release from dying or stressed cells, Ro-bound RNAs are proposed to contribute to these symptoms by associating with the antibodies and activating receptors that control the production of molecules that cause tissue damage. Studying how Ro functions in cells and identifying Ro-bound RNAs may make it possible to design drugs that specifically target either Ro or its associated RNA molecules.